AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icspA_bbur_opreg_300.orf -g0.282 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.282
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BB0436	172	DNA gyrase, subunit B (gyrB)

Motif number 1

CTTGTTGGTTTTAGCACTATACTTTTAACAT	1	20	1	TTAGCACTTA	    0.982432	-153
CACTATACTTTTAACATTATATAGTATAATG	1	34	1	TTAACATTTA	     0.99442	-139
GAATCCTAATTTAACATTATACTATATAATG	1	48	0	TTAACATTTA	     0.99442	-125
TAATGTTAAATTAGGATTCTATCTAAATTGT	1	60	1	TTAGGATTTA	    0.987726	-113
ACAGATAAATTCTACATTAAAAAAAAAATAA	1	135	0	TCTACATTAA	    0.952493	-38
TTTATCTGTGTCTAGATTTTAATTAA     	1	157	1	TCTAGATTTA	    0.976736	-16
          ******** **

Masking position 6
Map Score:   8.21255

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 69
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

CTATATAATGTTAAAAGTATAGTGCTAAAA	1	28	0	TTAAAAGTAT	    0.944244	-145
CTTTTAACATTATATAGTATAATGTTAAAT	1	41	1	TATATAGTAT	    0.955072	-132
GGATTCTATCTAAATTGTTTGTGAATTTTT	1	73	1	TAAATTGTTT	    0.944244	-100
TTGTGAATTTTTAAAAGTTTTTGGTATTTC	1	91	1	TTAAAAGTTT	    0.880103	-82
TCCTATGTAATAGATATTATTTTTTTTTTA	1	119	1	TAGATATTAT	     0.97438	-54
TTTTTTAATGTAGAATTTATCTGTGTCTAG	1	142	1	TAGAATTTAT	    0.959215	-31
TATCTGTGTCTAGATTTTAATTAA      	1	159	1	TAGATTTTAA	    0.840247	-14
          **********

Masking position 4
Map Score:   5.33373

Number of sites scoring better than the average of aligned sites = 779
Number in coding regions = 488
Number in noncoding regions = 291
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

AAACCAACAAGGACAAAAAA          	1	1	0	GGACAAAAAA	    0.961156	-172
TATAGTGCTAAAACCAACAAGGACAAAAAA	1	11	0	AAACCAACAA	    0.983189	-162
TTTTAAAAATTCACAAACAATTTAGATAGA	1	77	0	TCACAAACAA	    0.970732	-96
TACATAGGAAATACCAAAAACTTTTAAAAA	1	98	0	ATACCAAAAA	    0.968478	-75
ATTCTACATTAAAAAAAAAATAATATCTAT	1	128	0	AAAAAAAAAA	     0.90999	-45
TAAAATCTAGACACAGATAAATTCTACATT	1	148	0	ACACAGATAA	    0.936013	-25
          **********

Masking position 7
Map Score:   2.64617

Number of sites scoring better than the average of aligned sites = 793
Number in coding regions = 525
Number in noncoding regions = 268
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

          **********

No masking
Map Score:   1.51646e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   1.51646e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   1.51646e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0